The photosynthetic euglenoid genus Phacus is commonly found in freshwater; it is characterized by a rigid to semi‐rigid cell, usually flat with numerous small discoid chloroplasts without pyrenoids. To understand the phylogenetic relationships among Phacus species, we used combined cytoplasmic SSU and LSU rDNA and plastid‐encoded SSU and LSU rDNA sequence data from 82 strains, including seven Lepocinclis, three Discoplastis, one Eutreptia, and two Eutreptiella strains, as well as morphological data. The combined molecular dataset was analyzed using Bayesian and maximum likelihood methods. The resulting tree revealed that the genus Phacus was not monophyletic and fully resolved the phylogenetic relationships among eight lineages that were congruent with unique morphological characters in each clade. Molecular phylogeny and detailed morphological data led to the descriptions of seven new species: P. brevisulca, P. claviformis, P. hordei‐formis, P. longisulca, P. minimus, P. paraorbicularis, and P. viridioryza. The new species were well supported as independent species and formed close relationships with small Phacus species and P. orbicularis in the tree. In addition, the new species had unique molecular signatures and showed high genetic diversity. Although the strains of P. orbicularis sensu Hübner were morphologically very similar, the phylogenetic analyses and genetic diversity suggested that P. orbicularis sensu Hübner should be divided into two subclades.